Fig. 3

Initializing time course settings. (left) A graph containing two Time course nodes (called short and long). The node called ‘long’ inherits the settings from its parent, redefining some quantities with new values (local changes). (right top) ‘Short’ simulation configuration details. Duration and interval size are changed with respect to the basic default configuration determined by JC-RM. Other values, like the kind of simulation engine with its internal parameters, are left unchanged. (right bottom) ‘Long’ simulation configuration details. Duration and interval size are changed with respect to the inherited values. Since the two nodes are connected, the descendant values can be expressed in terms of any ascendant parameter, making the expression of the duration in this node highly flexible. Each Time Course node applies to a specific list of ‘Parameter sets’ as shown in the left portion of each window: in this case the short configuration is applied to both WT and WT_galactose while the long configuration is applied only to the WT_galactose node